Introduction: Prevention and treatment of overweight and obesity are easier in children than in adults. This study was conducted to evaluate the Smart Eating and Healthy Activity (SEHAT) programme, an intervention programme involving parents, teachers, and students in Indonesia to prevent obesity at schools. The intervention was conducted in the form of seminars and leaflets distribution to parents, training of teachers, training of student health cadres, training of students by trained teachers, health promotion to school canteen vendors, and promoting healthy home food weekly. Methods: This non-randomised controlled trial study was conducted from January to May 2016 in North Jakarta. The primary outcome was body mass index (BMI) changes measured with SECA® digital scale for weight and microtoise for height measurements. The secondary outcomes were changes in children’s knowledge, self-efficacy and behaviours, measured using self-made questionnaires, and physical activity using the Physical Activity Questionnaire for Older Children (PAQ-C). A total of 278 fourth and fifth-grade elementary school students aged 9 to 11 years old were recruited and grouped into intervention group (121 students) and control group (157 students). Results: The study reported a significant change between intervention and control groups on knowledge (1.28 vs 0.31), attitude (1.85 vs 0.06), physical activity (0.14 vs -0.32), eating fruits and vegetables (0.02 vs -0.78), and BMI (0.33 vs 0.71). Conclusion: The five-month SEHAT intervention programme effectively promoted knowledge on healthy eating and physical activity for obesity prevention by increasing physical activity, eating fruits and vegetables, and maintaining students’ BMI.